Contacts of the strand formed by residues 268 - 275 (chain A) in PDB entry 2J0M
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A ALA* 3.1 24.0 - - - -
262A LEU* 3.2 17.4 + - + +
266A TRP* 4.3 14.1 - - + +
267A ILE* 1.3 86.8 - - - +
269A SER* 1.3 74.1 - - - +
270A VAL* 3.5 17.6 + - + +
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Residues in contact with SER 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A CYS 3.5 8.4 + - - -
261A ALA* 4.6 2.6 - - - +
267A ILE* 4.4 0.7 + - - +
268A ILE* 1.3 76.8 - - - +
270A VAL* 1.3 66.2 + - - +
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A PHE 3.6 0.5 - - - +
259A LYS* 3.7 2.0 - - - -
260A CYS* 3.0 35.6 + - - +
261A ALA 4.5 0.2 - - - -
262A LEU* 3.8 35.9 - - + -
268A ILE* 3.9 20.0 - - + +
269A SER* 1.3 79.9 - - - +
271A GLU* 1.3 60.3 + - - +
272A LEU* 3.8 8.2 + - + -
282A TYR* 4.0 36.8 - - + -
283A LEU 4.8 4.0 - - - +
284A THR* 5.4 5.8 - - + -
285A ASP* 5.7 0.7 - - - -
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Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ARG* 4.8 0.5 + - - -
257A CYS* 3.5 26.3 - - + +
258A PHE 3.4 11.9 - - - +
259A LYS* 4.5 17.3 - - + +
270A VAL* 1.3 73.8 - - - +
272A LEU* 1.3 61.0 + - - +
282A TYR* 3.2 3.9 - - - -
283A LEU* 2.6 58.9 + - + +
285A ASP* 4.0 15.6 + - - +
286A LYS* 3.0 35.1 + - - -
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A GLU 3.6 1.6 - - - +
257A CYS* 3.1 10.3 - - - +
258A PHE* 2.7 47.0 + - + +
260A CYS* 3.6 16.2 - - - -
262A LEU* 4.6 11.9 - - + -
270A VAL* 3.8 9.2 + - + -
271A GLU* 1.3 73.2 - - - +
273A ALA* 1.3 59.7 + - - +
274A ILE* 3.9 8.9 + - + -
280A ILE* 3.9 25.1 - - + -
281A SER 3.1 21.3 - - - +
282A TYR* 3.9 13.2 - - + -
293A LEU* 4.7 3.4 - - + -
318A LEU* 6.6 0.2 - - + -
327A LEU* 6.5 0.4 - - + -
329A VAL* 4.8 12.1 - - + -
340A MET* 3.6 23.6 - - + -
344A ILE* 6.1 1.6 - - + -
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A LYS* 3.7 24.9 - - + -
256A GLU 3.7 4.0 - - - -
257A CYS* 4.1 4.9 - - - -
271A GLU 3.9 1.8 + - - -
272A LEU* 1.3 73.6 - - - +
274A ILE* 1.3 61.6 + - - +
275A GLY 4.0 0.7 - - - -
278A GLU* 4.5 6.4 - - + +
279A GLY 3.5 2.9 - - - +
280A ILE* 3.6 1.0 - - - -
281A SER* 2.8 47.0 + - - +
283A LEU* 3.7 25.6 - - + -
290A PRO* 5.5 0.2 - - + -
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A LYS* 3.3 3.5 - - - +
256A GLU* 2.9 33.7 + - - +
258A PHE* 3.7 27.6 - - + -
272A LEU* 4.4 8.7 - - + -
273A ALA* 1.3 75.7 - - - +
275A GLY* 1.3 60.0 + - - +
279A GLY 3.3 2.5 - - - +
280A ILE* 4.4 17.0 - - + -
296A PHE* 3.8 24.5 - - + -
340A MET* 4.3 17.5 - - + -
343A LEU* 3.6 33.7 - - + +
344A ILE* 4.5 17.7 - - + -
347A TYR* 4.0 9.1 + - + -
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Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A LYS* 3.8 4.9 - - - -
274A ILE* 1.3 76.8 - - - +
276A PRO* 1.3 71.4 - - - +
277A GLU 3.3 2.2 - - - -
278A GLU* 3.4 15.0 + - - -
279A GLY* 2.8 36.0 + - - +
296A PHE* 3.4 6.7 - - - -
347A TYR* 3.8 7.2 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il